Task accelerators in a HealthOmics workflow definition - AWS HealthOmics

AWS HealthOmics variant stores and annotation stores will no longer be open to new customers starting November 7th, 2025. If you would like to use variant stores or annotation stores, sign up prior to that date. Existing customers can continue to use the service as normal. For more information, see AWS HealthOmics variant store and annotation store availability change.

Task accelerators in a HealthOmics workflow definition

In the workflow definition, you can optionally specify the GPU accelerator-spec for a task. HealthOmics supports the following accelerator-spec values, along with the supported instance types:

Accelerator spec Healthomics instance types
nvidia-tesla-t4 G4
nvidia-tesla-t4-a10g G4 and G5
nvidia-tesla-a10g G5
nvidia-l4-a10g G5 and G6
nvidia-l4 G6
nvidia-l40s G6e

If you specify an accelerator type that supports multiple instance types, HealthOmics selects the instance type based on available capacity. If both instance types are available, HealthOmics gives preference to the lower cost instance.

For details about the instance types, see Accelerated-computing instances.

In the following example, the workflow definition specifies nvidia-l4 as the accelarator:

WDL
task my_task { runtime { ... acceleratorCount: 1 acceleratorType: "nvidia-l4" } ... }
NextFlow
process my_task { ... accelerator 1, type: "nvidia-l4" ... }
CWL
cwlVersion: v1.2 class: CommandLineTool requirements: ... cwltool:CUDARequirement: cudaDeviceCountMin: 1 cudaComputeCapability: "nvidia-l4" cudaVersionMin: "1.0"